Template developed with materials from https://hbctraining.github.io/main/.
This code is in this
revision.
Overview
- Project: name_hbcXXXXX
- PI: person name
- Analyst: person in the core
- Experiment: short description
- Aim: short description
MAST analysis
Pre-processing
Subset genes observed in at least 10% of cells …
Prep for MAST comparison …
MAST run with desired contrasts …
Output results …
[Full MAST object saved]
[MAST summary results output to csv files]
[Significant MAST summary results output to csv files]
Differentially
Expressed Genes Table
[Option 1: numbers displayed in digits]
[Option 2: FDR displayed in scientific notation]
Group
Mean Heatmap
age

Volcano plot and Top DEG
This volcano plot shows the genes that are significantly up- and
down-regulated as a result of the analysis comparison.
The points highlighted:
- in grey
points are non-significant.
- in blue
have a padj > 0.05 and a log2-fold change > 0.5.
- in plum have a
padj < 0.05 and a log2-fold change < 0.5.
- in purple are
genes that have fdr < 0.05 and a log2-fold change > 0.5.
The dashed lines correspond to the cutoff values of log2 foldchance
and padj that we have chosen.
age

% of
expression for Top DEGs

Plain
sc-expression across contrast groups: top 16 DEGs
HLA-B

SAT1

PERP

CD74

IGFBP5

KRT10

MT-CYB

MT-ND1

H2AFZ

ADIRF

CAV1

CCL19

CCL21

MT-ATP6

PFN1

TPPP3

Colored sc-expression across contrast groups: top 16 DEGs
HLA-B

SAT1

PERP

CD74

IGFBP5

KRT10

MT-CYB

MT-ND1

H2AFZ

ADIRF

CAV1

CCL19

CCL21

MT-ATP6

PFN1

TPPP3

Dot
styles: sc-expression across contrast groups
quasirandom

dotplot

jitter

R session
List and version of tools used for the QC report generation.